niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/spmregister.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPMREGISTER_METADATA = Metadata(
-    id="f037d545faca30a5ba9e5094c01f167e854b4f1f.boutiques",
+    id="631ca3c46e81cdbcc0721229103b0d1a0baf1404.boutiques",
     name="spmregister",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ SPMREGISTER_METADATA = Metadata(
 
 
 SpmregisterParameters = typing.TypedDict('SpmregisterParameters', {
-    "__STYXTYPE__": typing.Literal["spmregister"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/spmregister"]],
+    "subjid": str,
+    "mov": str,
+    "reg": str,
+    "frame": typing.NotRequired[float | None],
+    "mid_frame": bool,
+    "template_out": typing.NotRequired[str | None],
+    "fsvol": typing.NotRequired[str | None],
+    "force_ras": bool,
+    "outvol": typing.NotRequired[str | None],
+    "tmpdir": typing.NotRequired[str | None],
+    "nocleanup": bool,
+    "version": bool,
+    "help": bool,
+})
+SpmregisterParametersTagged = typing.TypedDict('SpmregisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/spmregister"],
     "subjid": str,
     "mov": str,
     "reg": str,
@@ -29,43 +45,11 @@ SpmregisterParameters = typing.TypedDict('SpmregisterParameters', {
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "spmregister": spmregister_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "spmregister": spmregister_outputs,
-    }.get(t)
 
 
 class SpmregisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `spmregister(...)`.
+    Output object returned when calling `SpmregisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +73,7 @@ def spmregister_params(
     nocleanup: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> SpmregisterParameters:
+) -> SpmregisterParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +100,7 @@ def spmregister_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "spmregister",
+        "@type": "freesurfer/spmregister",
         "subjid": subjid,
         "mov": mov,
         "reg": reg,
@@ -156,50 +140,50 @@ def spmregister_cargs(
     cargs.append("spmregister")
     cargs.extend([
         "--s",
-        params.get("subjid")
+        params.get("subjid", None)
     ])
     cargs.extend([
         "--mov",
-        params.get("mov")
+        params.get("mov", None)
     ])
     cargs.extend([
         "--reg",
-        params.get("reg")
+        params.get("reg", None)
     ])
-    if params.get("frame") is not None:
+    if params.get("frame", None) is not None:
         cargs.extend([
             "--frame",
-            str(params.get("frame"))
+            str(params.get("frame", None))
         ])
-    if params.get("mid_frame"):
+    if params.get("mid_frame", False):
         cargs.append("--mid-frame")
-    if params.get("template_out") is not None:
+    if params.get("template_out", None) is not None:
         cargs.extend([
             "--template-out",
-            params.get("template_out")
+            params.get("template_out", None)
         ])
-    if params.get("fsvol") is not None:
+    if params.get("fsvol", None) is not None:
         cargs.extend([
             "--fsvol",
-            params.get("fsvol")
+            params.get("fsvol", None)
         ])
-    if params.get("force_ras"):
+    if params.get("force_ras", False):
         cargs.append("--force-ras")
-    if params.get("outvol") is not None:
+    if params.get("outvol", None) is not None:
         cargs.extend([
             "--o",
-            params.get("outvol")
+            params.get("outvol", None)
         ])
-    if params.get("tmpdir") is not None:
+    if params.get("tmpdir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmpdir")
+            params.get("tmpdir", None)
         ])
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("--nocleanup")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -220,16 +204,18 @@ def spmregister_outputs(
     ret = SpmregisterOutputs(
         root=execution.output_file("."),
         registration_file=execution.output_file("register.dat"),
-        resampled_mov=execution.output_file(params.get("outvol")) if (params.get("outvol") is not None) else None,
+        resampled_mov=execution.output_file(params.get("outvol", None)) if (params.get("outvol") is not None) else None,
     )
     return ret
 
 
 def spmregister_execute(
     params: SpmregisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SpmregisterOutputs:
     """
+    spmregister
+    
     Registers a volume to its FreeSurfer anatomical using SPM's spm_coreg.
     
     Author: FreeSurfer Developers
@@ -238,10 +224,12 @@ def spmregister_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SpmregisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPMREGISTER_METADATA)
     params = execution.params(params)
     cargs = spmregister_cargs(params, execution)
     ret = spmregister_outputs(params, execution)
@@ -266,6 +254,8 @@ def spmregister(
     runner: Runner | None = None,
 ) -> SpmregisterOutputs:
     """
+    spmregister
+    
     Registers a volume to its FreeSurfer anatomical using SPM's spm_coreg.
     
     Author: FreeSurfer Developers
@@ -295,8 +285,6 @@ def spmregister(
     Returns:
         NamedTuple of outputs (described in `SpmregisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SPMREGISTER_METADATA)
     params = spmregister_params(
         subjid=subjid,
         mov=mov,
@@ -312,13 +300,13 @@ def spmregister(
         version=version,
         help_=help_,
     )
-    return spmregister_execute(params, execution)
+    return spmregister_execute(params, runner)
 
 
 __all__ = [
     "SPMREGISTER_METADATA",
     "SpmregisterOutputs",
-    "SpmregisterParameters",
     "spmregister",
+    "spmregister_execute",
     "spmregister_params",
 ]

niwrap_freesurfer/freesurfer/sratio.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SRATIO_METADATA = Metadata(
-    id="a0c61694880fb0d0ab8bc4437e881ebd40901b82.boutiques",
+    id="5677bab1e316327b9e1c66c023ddc455c4daf9a6.boutiques",
     name="sratio",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ SRATIO_METADATA = Metadata(
 
 
 SratioParameters = typing.TypedDict('SratioParameters', {
-    "__STYXTYPE__": typing.Literal["sratio"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/sratio"]],
+    "value_a": float,
+    "value_b": float,
+    "abs_flag": bool,
+    "mask_threshold": typing.NotRequired[float | None],
+})
+SratioParametersTagged = typing.TypedDict('SratioParametersTagged', {
+    "@type": typing.Literal["freesurfer/sratio"],
     "value_a": float,
     "value_b": float,
     "abs_flag": bool,
     "mask_threshold": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "sratio": sratio_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "sratio": sratio_outputs,
-    }.get(t)
 
 
 class SratioOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sratio(...)`.
+    Output object returned when calling `SratioParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def sratio_params(
     value_b: float,
     abs_flag: bool = False,
     mask_threshold: float | None = None,
-) -> SratioParameters:
+) -> SratioParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def sratio_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sratio",
+        "@type": "freesurfer/sratio",
         "value_a": value_a,
         "value_b": value_b,
         "abs_flag": abs_flag,
@@ -107,14 +82,14 @@ def sratio_cargs(
     """
     cargs = []
     cargs.append("sratio")
-    cargs.append(str(params.get("value_a")))
-    cargs.append(str(params.get("value_b")))
-    if params.get("abs_flag"):
+    cargs.append(str(params.get("value_a", None)))
+    cargs.append(str(params.get("value_b", None)))
+    if params.get("abs_flag", False):
         cargs.append("--abs")
-    if params.get("mask_threshold") is not None:
+    if params.get("mask_threshold", None) is not None:
         cargs.extend([
             "--mask-thresh",
-            str(params.get("mask_threshold"))
+            str(params.get("mask_threshold", None))
         ])
     return cargs
 
@@ -141,9 +116,11 @@ def sratio_outputs(
 
 def sratio_execute(
     params: SratioParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SratioOutputs:
     """
+    sratio
+    
     Tool to compute ratio A/B if A>B, -B/A if B>A, with options for absolute
     computation and threshold masking.
     
@@ -153,10 +130,12 @@ def sratio_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SratioOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SRATIO_METADATA)
     params = execution.params(params)
     cargs = sratio_cargs(params, execution)
     ret = sratio_outputs(params, execution)
@@ -172,6 +151,8 @@ def sratio(
     runner: Runner | None = None,
 ) -> SratioOutputs:
     """
+    sratio
+    
     Tool to compute ratio A/B if A>B, -B/A if B>A, with options for absolute
     computation and threshold masking.
     
@@ -188,21 +169,19 @@ def sratio(
     Returns:
         NamedTuple of outputs (described in `SratioOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SRATIO_METADATA)
     params = sratio_params(
         value_a=value_a,
         value_b=value_b,
         abs_flag=abs_flag,
         mask_threshold=mask_threshold,
     )
-    return sratio_execute(params, execution)
+    return sratio_execute(params, runner)
 
 
 __all__ = [
     "SRATIO_METADATA",
     "SratioOutputs",
-    "SratioParameters",
     "sratio",
+    "sratio_execute",
     "sratio_params",
 ]

niwrap_freesurfer/freesurfer/stat_normalize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 STAT_NORMALIZE_METADATA = Metadata(
-    id="539aab15bed68c488933181c1c8d2ed1041f0cb8.boutiques",
+    id="832d1e413c9b64b884398894111475c8095d3f30.boutiques",
     name="stat_normalize",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ STAT_NORMALIZE_METADATA = Metadata(
 
 
 StatNormalizeParameters = typing.TypedDict('StatNormalizeParameters', {
-    "__STYXTYPE__": typing.Literal["stat_normalize"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/stat_normalize"]],
+    "input_sv_prefix": str,
+    "output_sv_prefix": str,
+    "resolution": typing.NotRequired[float | None],
+    "field_of_view": typing.NotRequired[float | None],
+    "sph_avg": typing.NotRequired[str | None],
+    "xfm_file": typing.NotRequired[str | None],
+    "fix_xfm_flag": bool,
+    "float2int_option": typing.NotRequired[str | None],
+})
+StatNormalizeParametersTagged = typing.TypedDict('StatNormalizeParametersTagged', {
+    "@type": typing.Literal["freesurfer/stat_normalize"],
     "input_sv_prefix": str,
     "output_sv_prefix": str,
     "resolution": typing.NotRequired[float | None],
@@ -24,42 +35,11 @@ StatNormalizeParameters = typing.TypedDict('StatNormalizeParameters', {
     "fix_xfm_flag": bool,
     "float2int_option": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "stat_normalize": stat_normalize_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class StatNormalizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `stat_normalize(...)`.
+    Output object returned when calling `StatNormalizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def stat_normalize_params(
     xfm_file: str | None = None,
     fix_xfm_flag: bool = False,
     float2int_option: str | None = None,
-) -> StatNormalizeParameters:
+) -> StatNormalizeParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +73,7 @@ def stat_normalize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "stat_normalize",
+        "@type": "freesurfer/stat_normalize",
         "input_sv_prefix": input_sv_prefix,
         "output_sv_prefix": output_sv_prefix,
         "fix_xfm_flag": fix_xfm_flag,
@@ -126,34 +106,34 @@ def stat_normalize_cargs(
     """
     cargs = []
     cargs.append("stat_normalize")
-    cargs.append(params.get("input_sv_prefix"))
-    cargs.append(params.get("output_sv_prefix"))
-    if params.get("resolution") is not None:
+    cargs.append(params.get("input_sv_prefix", None))
+    cargs.append(params.get("output_sv_prefix", None))
+    if params.get("resolution", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("resolution"))
+            str(params.get("resolution", None))
         ])
-    if params.get("field_of_view") is not None:
+    if params.get("field_of_view", None) is not None:
         cargs.extend([
             "-f",
-            str(params.get("field_of_view"))
+            str(params.get("field_of_view", None))
         ])
-    if params.get("sph_avg") is not None:
+    if params.get("sph_avg", None) is not None:
         cargs.extend([
             "-S",
-            params.get("sph_avg")
+            params.get("sph_avg", None)
         ])
-    if params.get("xfm_file") is not None:
+    if params.get("xfm_file", None) is not None:
         cargs.extend([
             "-x",
-            params.get("xfm_file")
+            params.get("xfm_file", None)
         ])
-    if params.get("fix_xfm_flag"):
+    if params.get("fix_xfm_flag", False):
         cargs.append("-i")
-    if params.get("float2int_option") is not None:
+    if params.get("float2int_option", None) is not None:
         cargs.extend([
             "-c",
-            params.get("float2int_option")
+            params.get("float2int_option", None)
         ])
     return cargs
 
@@ -179,11 +159,13 @@ def stat_normalize_outputs(
 
 def stat_normalize_execute(
     params: StatNormalizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> StatNormalizeOutputs:
     """
-    This program will convert and average a sequence of volume-based statistics in
-    Talairach space.
+    stat_normalize
+    
+    This program will convert and average a sequence of volume-based statistics
+    in Talairach space.
     
     Author: FreeSurfer Developers
     
@@ -191,10 +173,12 @@ def stat_normalize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `StatNormalizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STAT_NORMALIZE_METADATA)
     params = execution.params(params)
     cargs = stat_normalize_cargs(params, execution)
     ret = stat_normalize_outputs(params, execution)
@@ -214,8 +198,10 @@ def stat_normalize(
     runner: Runner | None = None,
 ) -> StatNormalizeOutputs:
     """
-    This program will convert and average a sequence of volume-based statistics in
-    Talairach space.
+    stat_normalize
+    
+    This program will convert and average a sequence of volume-based statistics
+    in Talairach space.
     
     Author: FreeSurfer Developers
     
@@ -236,8 +222,6 @@ def stat_normalize(
     Returns:
         NamedTuple of outputs (described in `StatNormalizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(STAT_NORMALIZE_METADATA)
     params = stat_normalize_params(
         input_sv_prefix=input_sv_prefix,
         output_sv_prefix=output_sv_prefix,
@@ -248,13 +232,13 @@ def stat_normalize(
         fix_xfm_flag=fix_xfm_flag,
         float2int_option=float2int_option,
     )
-    return stat_normalize_execute(params, execution)
+    return stat_normalize_execute(params, runner)
 
 
 __all__ = [
     "STAT_NORMALIZE_METADATA",
     "StatNormalizeOutputs",
-    "StatNormalizeParameters",
     "stat_normalize",
+    "stat_normalize_execute",
     "stat_normalize_params",
 ]